Specific and Quantitative Assessment of Naphthalene and Salicylate Bioavailability by Using a Bioluminescent Catabolic Reporter Bacterium

Soil concentrations, compositional profiles, sources and bioavailability of polychlorinated dibenzo dioxins/furans, polychlorinated biphenyls and polycyclic aromatic hydrocarbons in open municipal dumpsites of Chennai city, India

Several studies have reported the release of halogenated persistent organic pollutants (POPs) and polycyclic aromatic hydrocarbons (PAHs) associated with open burning of municipal solid waste. Considering soil as a sink for such organic contaminants, we conducted an in-depth study on the surface soil concentrations of polychlorinated dibenzo-p-dioxins/furans (PCDD/Fs), polychlorinated biphenyls (PCBs) and sixteen USEPA enlisted PAHs collected from thirteen zones of the two major municipal dumpsites, Kodungaiyur dumpsite (KDS) and Perungudi dumpsite (PDS) of Chennai city. Indigenous microbes from dumpsite soil samples were isolated and identified based on 16S rRNA sequencing and phylogenetic analysis. Using indigenous microbes, we have elucidated the bioavailability of the targeted organic pollutants for each site.Range of Σ₁₇PCDD/Fs, Σ₂₅PCBs and ∑₁₆PAHs varied between 3.96-612 pg/g (96.0 pg/g; median), ND-182 ng/g (6.35 ng/g; median) and 0.62-3649 ng/g (64.3 ng/g; median), respectively. All the dumpsite samples showed bioavailability for POPs and PAHs. Toxicity equivalent values (TEQs) associated with dioxin-like PCBs and PCDD/Fs from the zones where dumped municipal solid wastes were collected from electronic-waste/IT-corridor/port areas and toxic PAHs from the zone receiving wastes from the industrial corridor of the city were higher than the soil permissible limit prescribed by the World Health Organization.

Repetitive Detection of Aromatic Hydrocarbon Contaminants with Bioluminescent Bioreporters Attached on Tapered Optical Fiber Elements

In this study, we show the repetitive detection of toluene on a tapered optical fiber element (OFE) with an attached layer of Pseudomonas putida TVA8 bioluminescent bioreporters. The bioluminescent cell layer was attached on polished quartz modified with (3-aminopropyl)triethoxysilane (APTES). The repeatability of the preparation of the optical probe and its use was demonstrated with five differently shaped OFEs. The intensity of measured bioluminescence was minimally influenced by the OFE shape, possessing transmittances between 1.41% and 5.00%. OFE probes layered with P. putida TVA8 were used to monitor liquid toluene over a two-week period. It was demonstrated that OFE probes layered with positively induced P. putida TVA8 bioreporters were reliable detectors of toluene. A toluene concentration of 26.5 mg/L was detected after <30 min after immersion of the probe in the toluene solution. Additional experiments also immobilized constitutively bioluminescent cells of E. coli 652T7, on OFEs with polyethyleneimine (PEI). These OFEs were repetitively induced with Lauria-Bertani (LB) nutrient medium. Bioluminescence appeared 15 minutes after immersion of the OFE in LB. A change in pH from 7 to 6 resulted in a decrease in bioluminescence that was not restored following additional nutrient inductions at pH 7. The E. coli 652T7 OFE probe was therefore sensitive to negative influences but could not be repetitively used.

A Minimized Chemoenzymatic Cascade for Bacterial Luciferase in Bioreporter Applications

Bacterial luciferase (Lux) catalyzes a bioluminescence reaction by using long-chain aldehyde, reduced flavin and molecular oxygen as substrates. The reaction can be applied in reporter gene systems for biomolecular detection in both prokaryotic and eukaryotic organisms. Because reduced flavin is unstable under aerobic conditions, another enzyme, flavin reductase, is needed to supply reduced flavin to the Lux-catalyzed reaction. To create a minimized cascade for Lux that would have greater ease of use, a chemoenzymatic reaction with a biomimetic nicotinamide (BNAH) was used in place of the flavin reductase reaction in the Lux system. The results showed that the minimized cascade reaction can be applied to monitor bioluminescence of the Lux reporter in eukaryotic cells effectively, and that it can achieve higher efficiencies than the system with flavin reductase. This development is useful for future applications as high-throughput detection tools for drug screening applications.

Surface-Adsorbed Contaminants Mediate the Importance of Chemotaxis and Haptotaxis for Bacterial Transport Through Soils

Chemotaxis and haptotaxis are important biological mechanisms that influence microbial movement toward concentrated chemoattractants in mobile liquids and along immobile surfaces, respectively. This study investigated their coupled effect, as induced by naphthalene (10 mg L⁻¹), on the transport and retention of two pollutant-degrading bacteria, Pseudomonas fluorescens 5RL (Pf5RL) and Pseudomonas stutzeri DQ1 (PsDQ1), in quartz sand and natural soil. The results demonstrated that PsDQ1 was not chemotactic, whereas Pf5RL was chemotactic at 25°C but not at 4°C due to the restricted movement. In a quartz sand column, haptotaxis did not play a role in increasing the transport of Pf5RL as compared with chemotaxis. Compared with a naphthalene-free soil column, Pf5RL broke through naphthalene-presaturated soil columns to reach a stable effluent concentration 0.5 pore volumes earlier due to advective chemotaxis occurring behind the plume front in the bulk solution. Pf5RL also demonstrated greater retention (e.g., a doubled rate of attachment and a one-third smaller breakthrough percentage) due to along-surface haptotaxis and near-surface chemotaxis occurring in less mobile water near the soil surface. However, both chemotaxis and haptotaxis were weakened when Pf5RL co-transported with naphthalene due to reduced adsorption of naphthalene on the soil. This study suggests that surface adsorption of naphthalene can mediate the relative importance of advective chemotaxis (facilitating initial breakthrough), near-surface chemotaxis (increasing bacterial collision), and haptotaxis (increasing bacterial residence time).

Development of a 2-Nitrobenzoate-Sensing Bioreporter Based on an Inducible Gene Cluster

Based on the sole information of structural genes of the 2-nitrobenzoate (2NBA) utilizing catabolic gene cluster (onbX1X2FCAR1EHJIGDBX3), 2NBA-sensing bioreporters were constructed by incorporating egfp into the onb gene cluster of Cupriavidus sp. strain ST-14. Incorporation of reporter gene in proximal to the hypothesized promoter region in conjunction with the disruption of the gene encoding inducer-metabolizing enzyme was turned out to be advantageous in reporter gene expression at low inducer concentration. The bioreporter strain was capable of expressing EGFP from the very 1st hour of induction and could detect 2NBA at (sub) nanomolar level exhibiting a strict specificity toward 2NBA, displaying no response to EGFP expression from its meta- and para-isomers as well as from a number of structurally related compounds. The present study is a successful demonstration of the development of a 2NBA-sensing bioreporter with respect to ease of construction, inducer specificity, and sensitivity, without prior knowledge of the associated inducer-responsive promoter-regulator elements. The present approach can be used as a model for the development of bioreporters for other environmental pollutants.

Quorum Sensing Disruption in Vibrio harveyi Bacteria by Clay Materials

This work describes the use of clay minerals as catalysts for the degradation of quorum sensing molecule N-(3-oxooctanoyl)-dl-homoserine lactone. Certain clay minerals as a result of their surface properties and porosity can catalytically degrade the quorum sensing molecule into smaller fragments. The disruption of quorum sensing by clay in a growing Gram-negative Vibrio harveyi bacteria culture was also studied by monitoring luminescence and population density of the bacteria, wherein quenching of bacterial quorum sensing activity was observed by means of luminescence reduction. The results of this study show that food-grade clays can be used as biocatalysts in disrupting bacterial activity in various media.

Responses of tall fescue (Festuca arundinacea) to growth in naphthalene-contaminated sand: xenobiotic stress versus water stress

The adaptations of tall fescue (Festuca arundinacea) arising from growth in naphthalene-contaminated sand (0.8 g kg(-1) sand dry weight (dw)) were investigated in the contexts of xenobiotic stress and water stress. The transfer of polycyclic aromatic hydrocarbons (PAHs) across the root endodermis was investigated using the hydrophobic Nile red stain as a PAH homologue. Nile red was applied to the epidermis of a living root to visualise uptake into the root through the transpiration stream, and the distance travelled by the stain into the root tissues was investigated using epi-fluorescence microscopy (Nikon Eclipse 90i). The results showed that the Nile red applied to the roots grown in naphthalene-contaminated sand was unable to penetrate the roots beyond the endodermis, whereas those grown in 'clean' sand showed evidence of uptake into the xylem vessels beyond the endodermis. Furthermore, partial collapse was observed in the cortex of naphthalene-treated roots, suggesting drought stress. Interestingly, the treated plants showed visual resilience to drought stress whilst the leaves of the control plants showed signs of wilting.

Changes in the abundance of sugars and sugar-like compounds in tall fescue (Festuca arundinacea) due to growth in naphthalene-treated sand

The hydrophilic metabolome of tall fescue (Festuca arundinacea) adapted to grow in naphthalene-treated sand (0.8 g kg(-1) sand dw) was analysed using gas chromatography-mass spectrometry, and peaks corresponding to the more abundant compounds were tentatively identified from analysis of their mass spectral features and reference to the NIST Mass Spectral Database. Particular attention was paid to sugars as they are known to play important roles as stress regulators in plants. The results showed that the abundance of sugars was greater in the roots but lesser in the shoots of treated plants when compared to their control counterparts. The results for indole acetic acid (IAA) were notable: IAA was prominently less in the treated roots compared to shoots, and in treated shoots, IAA was particularly subdued compared to untreated shoots consistent with IAA degradation in treated plant tissues. The differences in the molecular phenotype between control and treated plants were expressed in root structural differences. The treated roots were modified to have greater suberisation, enhanced thickening in the endodermis and distortions in the cortical zone as demonstrated through scanning electron and epi-fluorescence microscopy.

The influence of carbon sources on the expression of the recA gene and genotoxicity detection by an Acinetobacter bioreporter

Bacterial whole-cell bioreporters are practical and reliable analytical tools to assess the toxicity and bioavailability of environmental contaminants, yet evidence has shown that their performance could be affected by different carbon sources. This paper evaluated the influence of carbon sources on the recA gene (ACIAD1385) in a DNA damage-inducible recA::luxCDABE Acinetobacter bioreporter and optimized the induction conditions for its practical application in environmental monitoring. Different carbon sources, including LB, potassium acetate (MMA), sodium citrate (MMC), sodium pyruvate (MMP), and sodium succinate (MMS), significantly influenced (p < 0.05) the bioluminescence intensity of the genotoxicity bioreporter. A reverse transcription quantitative PCR (RT-qPCR) showed the different expression levels of the DNA damage-inducible gene recA (p < 0.05), suggesting that carbon sources influenced the DNA damage response in the Acinetobacter bioreporter at the transcriptional level. Additionally, proteomic analysis identified 122 proteins that were differentially expressed after exposure to mitomycin C in defined media and LB, and 5 of them were related to the DNA damage response, indicating the effects of carbon sources on the DNA damage response in Acinetobacter at the translational level. The repression effect caused by the rich medium, LB, was possibly related to the mechanism of carbon catabolite repression. Our results suggest that the practical application of Acinetobacter bioreporters to the genotoxicity assessment of polycyclic aromatic hydrocarbon (PAH)-contaminated soils could be significantly improved by using a standard medium of defined composition, as this could increase their sensitivity.

Mathematical model for cyclodextrin alteration of bioavailability of organic pollutants

While many cyclodextrin-based applications have been developed to assess or enhance bioavailability of organic pollutants, the choice of cyclodextrin (CD) is largely empirical, with little consideration of pollutant diversity and environmental matrix effects. This study aimed at developing a mathematical model for quantifying CD alteration of bioavailability of organic pollutants. Cyclodextrin appears to have multiple effects, together contributing to its bioavailability-enhancing property. Cyclodextrin is adsorbed onto the adsorbent matrix to different extents. The adsorbed CD is capable of sequestrating organic pollutants, highlighting the role of a pseudophase similar to solid environmental matrix. Aqueous CD can reduce adsorption of organic pollutants via inclusion complexation. The two effects cancel each other to a certain degree, which determines the levels of organic pollutants dissolved (comprising freely dissolved and CD-included forms). Additionally, the CD-included form is nearly identical in biological activity to the free form. A mathematical model of one variable (i.e., CD concentration) was derived to quantify effects of CD on the bioavailability of organic pollutants. Model analysis indicates that alteration of bioavailability of organic pollutants by CD depends on both CD (type and level) and environmental matrix. The selection of CD type and amendment level for a given application may be predicted by the model.

Genetically modified whole-cell bioreporters for environmental assessment

Living whole-cell bioreporters serve as environmental biosentinels that survey their ecosystems for harmful pollutants and chemical toxicants, and in the process act as human and other higher animal proxies to pre-alert for unfavorable, damaging, or toxic conditions. Endowed with bioluminescent, fluorescent, or colorimetric signaling elements, bioreporters can provide a fast, easily measured link to chemical contaminant presence, bioavailability, and toxicity relative to a living system. Though well tested in the confines of the laboratory, real-world applications of bioreporters are limited. In this review, we will consider bioreporter technologies that have evolved from the laboratory towards true environmental applications, and discuss their merits as well as crucial advancements that still require adoption for more widespread utilization. Although the vast majority of environmental monitoring strategies rely upon bioreporters constructed from bacteria, we will also examine environmental biosensing through the use of less conventional eukaryotic-based bioreporters, whose chemical signaling capacity facilitates a more human-relevant link to toxicity and health-related consequences.

Pseudomonas fluorescens HK44: lessons learned from a model whole-cell bioreporter with a broad application history

Initially described in 1990, Pseudomonas fluorescens HK44 served as the first whole-cell bioreporter genetically endowed with a bioluminescent (luxCDABE) phenotype directly linked to a catabolic (naphthalene degradative) pathway. HK44 was the first genetically engineered microorganism to be released in the field to monitor bioremediation potential. Subsequent to that release, strain HK44 had been introduced into other solids (soils, sands), liquid (water, wastewater), and volatile environments. In these matrices, it has functioned as one of the best characterized chemically-responsive environmental bioreporters and as a model organism for understanding bacterial colonization and transport, cell immobilization strategies, and the kinetics of cellular bioluminescent emission. This review summarizes the characteristics of P. fluorescens HK44 and the extensive range of its applications with special focus on the monitoring of bioremediation processes and biosensing of environmental pollution.

The evolution of the bacterial luciferase gene cassette (lux) as a real-time bioreporter

The bacterial luciferase gene cassette (lux) is unique among bioluminescent bioreporter systems due to its ability to synthesize and/or scavenge all of the substrate compounds required for its production of light. As a result, the lux system has the unique ability to autonomously produce a luminescent signal, either continuously or in response to the presence of a specific trigger, across a wide array of organismal hosts. While originally employed extensively as a bacterial bioreporter system for the detection of specific chemical signals in environmental samples, the use of lux as a bioreporter technology has continuously expanded over the last 30 years to include expression in eukaryotic cells such as Saccharomyces cerevisiae and even human cell lines as well. Under these conditions, the lux system has been developed for use as a biomedical detection tool for toxicity screening and visualization of tumors in small animal models. As the technologies for lux signal detection continue to improve, it is poised to become one of the first fully implantable detection systems for intra-organismal optical detection through direct marriage to an implantable photon-detecting digital chip. This review presents the basic biochemical background that allows the lux system to continuously autobioluminesce and highlights the important milestones in the use of lux-based bioreporters as they have evolved from chemical detection platforms in prokaryotic bacteria to rodent-based tumorigenesis study targets. In addition, the future of lux imaging using integrated circuit microluminometry to image directly within a living host in real-time will be introduced and its role in the development of dose/response therapeutic systems will be highlighted.

Online monitoring of water toxicity by use of bioluminescent reporter bacterial biochips

We describe a flow-through biosensor for online continuous water toxicity monitoring. At the heart of the device are disposable modular biochips incorporating agar-immobilized bioluminescent recombinant reporter bacteria, the responses of which are probed by single-photon avalanche diode detectors. To demonstrate the biosensor capabilities, we equipped it with biochips harboring both inducible and constitutive reporter strains and exposed it to a continuous water flow for up to 10 days. During these periods we challenged the biosensor with 2-h pulses of water spiked with model compounds representing different classes of potential water pollutants, as well as with a sample of industrial wastewater. The biosensor reporter panel detected all simulated contamination events within 0.5-2.5 h, and its response was indicative of the nature of the contaminating chemicals. We believe that a biosensor of the proposed design can be integrated into future water safety and security networks, as part of an early warning system against accidental or intentional water pollution by toxic chemicals.

Microbial whole-cell arrays

The coming of age of whole‐cell biosensors, combined with the continuing advances in array technologies, has prepared the ground for the next step in the evolution of both disciplines – the whole‐cell array. In the present review, we highlight the state‐of‐the‐art in the different disciplines essential for a functional bacterial array. These include the genetic engineering of the biological components, their immobilization in different polymers, technologies for live cell deposition and patterning on different types of solid surfaces, and cellular viability maintenance. Also reviewed are the types of signals emitted by the reporter cell arrays, some of the transduction methodologies for reading these signals and the mathematical approaches proposed for their analysis. Finally, we review some of the potential applications for bacterial cell arrays, and list the future needs for their maturation: a richer arsenal of high‐performance reporter strains, better methodologies for their incorporation into hardware platforms, design of appropriate detection circuits, the continuing development of dedicated algorithms for multiplex signal analysis and – most importantly – enhanced long‐term maintenance of viability and activity on the fabricated biochips.

Are luminescent bacteria suitable for online detection and monitoring of toxic compounds in drinking water and its sources?

Biosensors based on luminescent bacteria may be valuable tools to monitor the chemical quality and safety of surface and drinking water. In this review, an overview is presented of the recombinant strains available that harbour the bacterial luciferase genes luxCDABE, and which may be used in an online biosensor for water quality monitoring. Many bacterial strains have been described for the detection of a broad range of toxicity parameters, including DNA damage, protein damage, membrane damage, oxidative stress, organic pollutants, and heavy metals. Most lux strains have sensitivities with detection limits ranging from milligrams per litre to micrograms per litre, usually with higher sensitivities in compound-specific strains. Although the sensitivity of lux strains can be enhanced by various molecular manipulations, most reported detection thresholds are still too high to detect levels of individual contaminants as they occur nowadays in European drinking waters. However, lux strains sensing specific toxic effects have the advantage of being able to respond to mixtures of contaminants inducing the same effect, and thus could be used as a sensor for the sum effect, including the effect of compounds that are as yet not identified by chemical analysis. An evaluation of the suitability of lux strains for monitoring surface and drinking water is therefore provided.

Bioluminescence of Pseudomonas fluorescens HK44 in the course of encapsulation into silica gel. Effect of methanol

The bioluminescence (BLM) and colony-forming units (CFU) of Pseudomonas fluorescens HK44 were monitored during encapsulation into pre-polymerized Si(OMe)₄. The non-induced BLM of free cells was increased in the presence of 0.5-2.5 % MeOH. After mixing silica sol with the cell suspension, both BLM and CFU dropped to 1-3 and 8-18 %, respectively; both remained lowered as long as the silica biofilm contained residual MeOH. The kinetics of MeOH being released from silica biofilms (a thickness of 2-6 mm) were first-order. The decrease of bacterial activity due to encapsulation was proportional to the biofilm thickness. MeOH evolving during encapsulation is probably the principal stress factor but not the only one.

Automatic formation of hypotheses on the relationships between structure of naphthalene analogs and bioluminescence response of bioreporter Pseudomonas fluorescens HK44

Seven hypotheses on relationships between the structure of naphthalene analogs and bioluminescence response of bioreporter Pseudomonas fluorescens were formulated using GUHA (General Unary Hypotheses Automaton) on a training set of 37 compounds. Prediction of bioluminescence response of 12 new naphthalene analogs was successful in 69 % cases and resulted in rejection of single hypothesis. The results demonstrate applicability of GUHA in structure-activity research, especially for qualitative data.

Genetically modified Pseudomonas biosensing biodegraders to detect PCB and chlorobenzoate bioavailability and biodegradation in contaminated soils

Whole cell microbial biosensors offer excellent possibilities for assaying the complex nature of the bioavailable and bioaccessible fraction of pollutants in contaminated soils, which currently cannot be easily addressed. This paper describes the application and evaluation of three microbial biosensor strains designed to detect the bioavailability and biodegradation of PCBs (and end-products) in contaminated soils and sediments. Polychlorinated biphenyls (PCBs) are considered to be one of the most wide spread, hazardous and persistent pollutants. Herein we describe that there was a positive correlation between the PCB levels within the samples and the percentage of biosensor cells that were expressing their reporter gene; gfp. Immobilisation of the biosensors in calcium alginate beads allowed easy and accurate detection of the biosensor strains in contaminated soil and sludge samples. The biosensors also showed that PCB degradation activity was occurring at a much greater level in Pea inoculated planted soil compared to inoculated unplanted soil indicating rhizoremediation (the removal of pollutants by plant root associated microbes) shows considerable promise as a solution for removing organic xenobiotics from the environment.

Whole-cell fluorescent biosensors for bioavailability and biodegradation of polychlorinated biphenyls

Whole-cell microbial biosensors are one of the newest molecular tools used in environmental monitoring. Such biosensors are constructed through fusing a reporter gene such as lux, gfp or lacZ, to a responsive promoter. There have been many reports of the applications of biosensors, particularly their use in assaying pollutant toxicity and bioavailability. This paper reviews the basic concepts behind the construction of whole-cell microbial biosensors for pollutant monitoring, and describes the applications of two such biosensors for detecting the bioavailability and biodegradation of Polychlorinated Biphenyls (PCBs).

Microbial cell arrays

The coming of age of whole-cell biosensors, combined with the continuing advances in array technologies, has prepared the ground for the next step in the evolution of both disciplines - the whole cell array. In the present chapter, we highlight the state-of-the-art in the different disciplines essential for a functional bacterial array. These include the genetic engineering of the biological components, their immobilization in different polymers, technologies for live cell deposition and patterning on different types of solid surfaces, and cellular viability maintenance. Also reviewed are the types of signals emitted by the reporter cell arrays, some of the transduction methodologies for reading these signals, and the mathematical approaches proposed for their analysis. Finally, we review some of the potential applications for bacterial cell arrays, and list the future needs for their maturation: a richer arsenal of high-performance reporter strains, better methodologies for their incorporation into hardware platforms, design of appropriate detection circuits, the continuing development of dedicated algorithms for multiplex signal analysis, and - most importantly - enhanced long term maintenance of viability and activity on the fabricated biochips.

Characterization of an isoproturon mineralizing bacterial culture enriched from a French agricultural soil

The phenylurea herbicide isoproturon, 3-(4-isopropylphenyl)-1,1-dimethylurea (IPU), was found to be rapidly mineralized by a bacterial culture isolated from an agricultural soil regularly exposed to IPU. Molecular analysis of the bacterial culture by DNA fingerprinting, cloning and sequencing of the 16S rRNA genes revealed that it consisted of six different members among whom the dominant was related to Sphingomonas sp. Six bacterial strains belonging to genera Ancylobacter, Pseudomonas, Stenotrophomonas, Methylobacterium, Variovorax and Agrobacterium were isolated from the IPU-degrading culture. None of these were able to degrade IPU in pure culture and only the intact culture sustained the ability to mineralize IPU. The composition of the culture appeared stable suggesting that yet unknown interactions are involved in the IPU mineralization. IPU degradation involved the transitory accumulation of three known IPU metabolites 3-(4-isopropylphenyl)-1-methylurea, 3-(4-isopropylphenyl)-urea, and 4-isopropylaniline and their further degradation. Thus, it indicates a metabolic pathway initiated by two successive N-demethylations, followed by cleavage of the urea side chain. This culture did not degrade other structurally related phenylurea herbicides. The degrading activity of the bacterial culture was deeply influenced by the pH, being completely inhibited at pH 5.5 and optimal at pH 7.5.

Diversity, abundance, and consistency of microbial oxygenase expression and biodegradation in a shallow contaminated aquifer

The diversity of Rieske dioxygenase genes and short-term temporal variability in the abundance of two selected dioxygenase gene sequences were examined in a naphthalene-rich, coal tar waste-contaminated subsurface study site. Using a previously published PCR-based approach (S. M. Ní Chadhain, R. S. Norman, K. V. Pesce, J. J. Kukor, and G. J. Zylstra, Appl. Environ. Microbiol. 72:4078-4087, 2006) a broad suite of genes was detected, ranging from dioxygenase sequences associated with Rhodococcus and Sphingomonas to 32 previously uncharacterized Rieske gene sequence clone groups. The nag genes appeared frequently (20% of the total) in two groundwater monitoring wells characterized by low ( approximately 10(2) ppb; approximately 1 muM) ambient concentrations of naphthalene. A quantitative competitive PCR assay was used to show that abundances of nag genes (and archetypal nah genes) fluctuated substantially over a 9-month period. To contrast short-term variation with long-term community stability, in situ community gene expression (dioxygenase mRNA) and biodegradation potential (community metabolism of naphthalene in microcosms) were compared to measurements from 6 years earlier. cDNA sequences amplified from total RNA extracts revealed that nah- and nag-type genes were expressed in situ, corresponding well with structural gene abundances. Despite evidence for short-term (9-month) shifts in dioxygenase gene copy number, agreement in field gene expression (dioxygenase mRNA) and biodegradation potential was observed in comparisons to equivalent assays performed 6 years earlier. Thus, stability in community biodegradation characteristics at the hemidecadal time frame has been documented for these subsurface microbial communities.

Application of a luminescence-based biosensor for assessing naphthalene biodegradation in soils from a manufactured gas plant

Despite numerous reviews suggesting that microbial biosensors could be used in many environmental applications, in reality they have failed to be used for which they were designed. In part this is because most of these sensors perform in an aqueous phase and a buffered medium, which is in contrast to the nature of genuine environmental systems. In this study, a range of non-exhaustive extraction techniques (NEETs) were assessed for (i) compatibility with a naphthalene responsive biosensor and (ii) correlation with naphthalene biodegradation. The NEETs removed a portion of the total soil naphthalene in the order of methanol > HPCD > betaCD > water. To place the biosensor performance to NEETs in context, a biodegradation experiment was carried out using historically contaminated soils. By coupling the HPCD extraction with the biosensor, it was possible to assess the fraction of the naphthalene capable of undergoing microbial degradation in soil.

Toxicant identification by a luminescent bacterial bioreporter panel: application of pattern classification algorithms

Genetically engineered microorganisms, tailored to respond by a dose-dependent signal to the presence of toxic chemicals, are a potentially useful tool for environmental monitoring. One manifestation of this approach is based on a panel of luminescent bacterial bioreporters, harboring fusions of the luxCDABE operon to various stress-responsive gene promoters. Such sensors can report by a dose-dependent luminescent signal on the stress sensed by the cells and thus on the presence of toxic compound(s), but they lack the ability to identify the chemicals involved. Here, we demonstrate how the use of a panel of such sensors might offer a solution to this drawback. Five selected Escherichia coli reporter strains harboring fusions of selected gene promoters (grpE, nhoA, oraA, lacZ, and mipA) to luxCDABE were exposed to five model toxicants and to a toxicant-free control in a 40-repetition format. Each of the six treatments activated different promoters to different extents, producing its own unique fingerprint. Two machine learning schemes were challenged with the obtained data set: Bayesian decision theory and the nonparametric nearest-neighbor technique. The Bayesian classifiers performed better and were able to identify the sample's contents within 30 min with an error rate estimate that did not exceed 3% at a 95% confidence level and with zero false negatives. Performance in tap water and wastewater samples was similar. Given the coming of age of whole-cell sensing devices, pattern classification algorithms such as the ones described here offer a step toward the incorporation of reporter cells into future biosensor formats, including whole-cell arrays.

Response of the bioluminescent bioreporterPseudomonas fluorescens HK44 to analogs of naphthalene and salicylic acid

Pseudomonasfluorescens HK44 is a lux-based bioluminescent bioreporter capable of selective luminescence in the presence of naphthalene and/or salicylic acid intermediate of its metabolism. We attempted to induce bioluminescence (BL) in this strain with 72 compounds, viz. substituted naphthalenes, naphthalene-like compounds (e.g., quinoline), substituted salicylic acids, salicylic acid-like compounds (e.g., 2-anthranilic acid), oligocyclic aromates, and intermediates of naphthalene metabolism to better discriminate response specificity. From them, 42 induced BL significantly lower as compared to naphthalene, three (viz. isoquinoline, o-cresol, and salicylamide) induced BL significantly greater than naphthalene, and 27 yielded no bioluminescent response whatsoever. Strain HK44 is therefore not prone to extensive false-positive signaling and can serve as a fairly specific indicator organism for naphthalene bioavailability. At elevated concentrations, 41 compounds inhibited BL. Thus, the inclusion of constitutive bioreporter controls as indicators of sample toxicity is vital to successful biosensing application.

Analysis of bioavailable phenols from natural samples by recombinant luminescent bacterial sensors

A whole-cell recombinant bacterial sensor for the detection of phenolic compounds was constructed and used for the analysis of bioavailable phenols in natural samples. The sensor Pseudomonas fluorescens OS8(pDNdmpRlux) contains luxCDABE operon as a reporter under the control of phenol-inducible Po promoter from Pseudomonas sp. CF600. Expression of lux genes from the Po promoter, and thus the production of bioluminescence is controlled by the transcriptional activator DmpR, which initiates transcription in the presence of phenolic compounds. To take into account possible quenching (turbidity, toxicity) and/or stimulating effects of the environmental samples on the bacterial luminescence, control bacteria comparable to the sensors but lacking the phenol recognising elements were constructed and used in parallel in assays. The sensor bacteria were inducible with phenol, methylphenols, 2,3-, 2,4-, 2,6- and 3,4-dimethylphenol, resorcinol and 5-methylresorcinol but not with 2,5-dimethylresorcinol. The detection limits for different phenols varied from 0.03 mg/l (2-methylphenol) to 42.7 mg/l (5-methylresorcinol), being 0.08 mg/l for phenol, the most abundant phenolic contaminant in the environment. Different phenolic compounds had an additive effect on the inducibility of the sensor. The constructed sensor bacteria were applied on groundwaters and semi-coke leachates to estimate the bioavailable fraction of phenols. The sensor-determined amount of phenols in different samples varied from 6% to 95% of total phenol content depending on the nature of the sample. As the phenol-recognising unit in the sensor originates from a natural phenol biodegradation pathway, the sensor-determined amount of phenols corresponds to the biodegradable amount of phenolic pollutants in the samples and therefore this sensor could be used to estimate the natural biodegradation potential of phenolic compounds in the complex environmental mixtures and matrixes.

Whole-cell living biosensors—are they ready for environmental application?

Since the development of the first whole-cell living biosensor or bioreporter about 15 years ago, construction and testing of new genetically modified microorganisms for environmental sensing and reporting has proceeded at an ever increasing rate. One and a half decades appear as a reasonable time span for a new technology to reach the maturity needed for application and commercial success. It seems, however, that the research into cellular biosensors is still mostly in a proof-of-principle or demonstration phase and not close to extensive or commercial use outside of academia. In this review, we consider the motivations for bioreporter developments and discuss the suitability of extant bioreporters for the proposed applications to stimulate complementary research and to help researchers to develop realistic objectives. This includes the identification of some popular misconceptions about the qualities and shortcomings of bioreporters.

Non-exhaustive extraction techniques (NEETs) for the prediction of naphthalene mineralisation in soil

Non-exhaustive extraction techniques (NEETs) have been shown to measure the putatively bioavailable fraction of hydrophobic compounds in soil. To date, these studies have only considered bioavailability in a single soil type. In this study, naphthalene was amended into five different soil types and mineralisation, bacterial biosensor response and the number of indigenous microbial naphthalene degraders were determined. Two NEETs were used to extract the naphthalene from soil; hydroxypropyl-beta-cyclodextrin (HPCD) and XAD-4. The HPCD extractable fraction correlated closely (R2 = 0.917) with the portion that was mineralised, but the XAD-4 extract did not (R2 = 0.044). HPCD may be ideal for the rapid assessment of the fraction of a hydrophobic organic contaminant that is available for biodegradation. A NEET that complements environmental microbial analysis will enhance our understanding of soil pollution interactions and equip us better in designing risk assessment models that integrate biological parameters. This application, although refined for soil samples, should be transferable to other environmental matrices.

Biosensor-based diagnostics of contaminated groundwater: assessment and remediation strategy

Shallow groundwater beneath a former airfield site in southern England has been heavily contaminated with a wide range of chlorinated solvents. The feasibility of using bacterial biosensors to complement chemical analysis and enable cost-effective, and focussed sampling has been assessed as part of a site evaluation programme. Five different biosensors, three metabolic (Vibrio fischeri, Pseudomonas fluorescens 10568 and Escherichia coli HB101) and two catabolic (Pseudomonas putida TVA8 and E. coli DH5alpha), were employed to identify areas where the availability and toxicity of pollutants is of most immediate environmental concern. The biosensors used showed different sensitivities to each other and to the groundwater samples tested. There was generally a good agreement with chemical analyses. The potential efficacy of remediation strategies was explored by coupling sample manipulation to biosensor tests. Manipulation involved sparging and charcoal treatment procedures to simulate remediative engineering solutions. Sparging was sufficient at most locations.

Illuminating the detection chain of bacterial bioreporters

Engineering bacteria for measuring chemicals of environmental or toxicological concern (bioreporter bacteria) has grown slowly into a mature research area. Despite many potential advantages, current bioreporters do not perform well enough to comply with environmental detection standards. Basically, the reasons for this are the lack of engineering principles in the detection chain in the bioreporters. Here, we dissect critical steps in the detection chain and illustrate how bioreporter design could be improved by mutagenizing specificity and selectivity of the sensing and regulatory proteins, by newer expression strategies and application of different signalling networks. Furthermore, we describe how redesigning bioreporter assays with respect to pollutant transport into the cells and application of other detection devices can decrease detection limits and increase the speed of detection.

Measurement of biologically available naphthalene in gas and aqueous phases by use of a Pseudomonas putida biosensor

Genetically constructed microbial biosensors for measuring organic pollutants are mostly applied in aqueous samples. Unfortunately, the detection limit of most biosensors is insufficient to detect pollutants at low but environmentally relevant concentrations. However, organic pollutants with low levels of water solubility often have significant gas-water partitioning coefficients, which in principle makes it possible to measure such compounds in the gas rather than the aqueous phase. Here we describe the first use of a microbial biosensor for measuring organic pollutants directly in the gas phase. For this purpose, we reconstructed a bioluminescent Pseudomonas putida naphthalene biosensor strain to carry the NAH7 plasmid and a chromosomally inserted gene fusion between the sal promoter and the luxAB genes. Specific calibration studies were performed with suspended and filter-immobilized biosensor cells, in aqueous solution and in the gas phase. Gas phase measurements with filter-immobilized biosensor cells in closed flasks, with a naphthalene-contaminated aqueous phase, showed that the biosensor cells can measure naphthalene effectively. The biosensor cells on the filter responded with increasing light output proportional to the naphthalene concentration added to the water phase, even though only a small proportion of the naphthalene was present in the gas phase. In fact, the biosensor cells could concentrate a larger proportion of naphthalene through the gas phase than in the aqueous suspension, probably due to faster transport of naphthalene to the cells in the gas phase. This led to a 10-fold lower detectable aqueous naphthalene concentration (50 nM instead of 0.5 micro M). Thus, the use of bacterial biosensors for measuring organic pollutants in the gas phase is a valid method for increasing the sensitivity of these valuable biological devices.

The potential of site-specific recombinases as novel reporters in whole-cell biosensors of pollution

DNA recombinases show some promise as reporters of pollutants providing that appropriate promoters are used and that the apparent dependence of expression on cell density can be solved. Further work is in progress using different recombinases and other promoters to optimize recombinase expression as well as to test these genetic constructs in contaminated environmental samples such as soil and water. It may be that a graded response reflecting pollutant concentration may not be possible. However, they show great promise for providing definitive detection systems for the presence of a pollutant and may be applicable to address the problem of bioavailability of pollutants in complex environments such as soil.

Development of bespoke bioluminescent reporters with the potential for in situ deployment within a phenolic-remediating wastewater treatment system

A suite of ecologically relevant, site-specific bioreporters was constructed by transposon mutagenesis of microorganisms isolated from a polluted phenolic-remediating wastewater treatment system. Four Pseudomonad species were engineered to carry a stable chromosomal copy of the lux operon (luxCDABE) derived from Photorhabdus luminescens. These recombinant reporter microorganisms were tested for bioluminescence response to relevant phenol concentrations in the laboratory and to phenolic-containing effluents generated by an industrial wastewater treatment plant. The reporters displayed proportional responses of bioluminescence decay with increasing phenol concentrations up to 800 mg l(-1) of phenol. When deployed against samples from the treatment system, they showed superior operational range and sensing capabilities to that observed for industry standard microorganisms such as Vibrio fischeri. Specifically, the engineered strains accurately predicted toxicity shifts in all the treatment compartments under study (with phenolic concentrations ranging from approximately 10 to 600 mg l(-1)) with a low coefficient of variation of replicate determinations (between 1.16% and 8.32%). This work highlights the utility of genetic modification of native microorganisms from sites of interest to provide robust and ecologically relevant organism-based reagents for toxicity monitoring with the potential for in situ deployment.

Effect of temperature, pH, and initial cell number on luxCDABE and nah gene expression during naphthalene and salicylate catabolism in the bioreporter organism Pseudomonas putida RB1353

One limitation of employing lux bioreporters to monitor in situ microbial gene expression in dynamic, laboratory-scale systems is the confounding variability in the luminescent responses. For example, despite careful control of oxygen tension, growth stage, and cell number, luminescence from Pseudomonas putida RB1353, a naphthalene-degrading lux bioreporter, varied by more than sevenfold during saturated flow column experiments in our laboratory. Therefore, this study was conducted to determine what additional factors influence the luminescent response. Specifically, this study investigated the impact of temperature, pH, and initial cell number (variations within an order of magnitude) on the peak luminescence of P. putida RB1353 and the maximum degradation rate (V(max)) during salicylate and naphthalene catabolism. Statistical analyses based on general linear models indicated that under constant oxygen tension, temperature and pH accounted for 98.1% of the variability in luminescence during salicylate catabolism and 94.2 and 49.5% of the variability in V(max) during salicylate and naphthalene catabolism, respectively. Temperature, pH, and initial substrate concentration accounted for 99.9% of the variability in luminescence during naphthalene catabolism. Initial cell number, within an order of magnitude, did not have a significant influence on either peak luminescence or V(max) during salicylate and naphthalene catabolism. Over the ranges of temperature and pH evaluated, peak luminescence varied by more than 4 orders of magnitude. The minimum parameter deviation required to alter lux gene expression during salicylate and naphthalene catabolism was a change in temperature of 1 degrees C, a change in pH of 0.2, or a change in initial cell number of 1 order of magnitude. Results from this study indicate that there is a need for careful characterization of the impact of environmental conditions on both the expression of the reporter and catabolic genes and the activities of the gene products. For example, even though lux gene expression was occurring at approximately 35 degrees C, the luciferase enzyme was inactive. Furthermore, this study demonstrates that with careful characterization and standardization of measurement conditions, the attainment of a reproducible luminescent response and an understanding of the response are feasible.

Kinetic analysis of bacterial bioluminescence

Bioluminescence from the lux-based bacterial reporter Pseudomonas fluorescens HK44 was experimentally investigated under growth substrate-rich and limiting conditions in batch, continuous stirred tank (CSTR), and turbidostat reactors. A mechanistically based, mathematical model was developed to describe bioluminescence based on 1) production and decay of catalytic enzymes, and 2) reactant cofactor availability. In the model, bioluminescence was a function of inducer, growth substrate, and biomass concentration. A saturational dependence on growth substrate concentration accommodated dependence on cofactor availability and inducer concentration to accommodate enzyme production was incorporated in the model. Under growth substrate and inducer limiting conditions in the batch reactor and CSTR, bioluminescence was found to decrease in response to cellular energy limitations. The effective lux system enzyme decay rate was determined in independent measurements to be 0.35 hr(-1) and the model captured most of the bioluminescent behavior, except at long growth times and high cell density.

A toxicity testing protocol using a bioluminescent reporter bacterium from activated sludge

A protocol for production, storage, and use of Shock 1 (Shk1) bioreporter cells for toxicity monitoring in wastewater treatment facilities was developed. Shk1 is a bioluminescent toxicity bioreporter for activated sludge previously constructed by the incorporation of lux genes into an activated sludge microorganism.A number of factors affecting Shk1 growth and bioluminescence were examined including the growth medium, tetracycline concentration, storage conditions, and test media. Based on the results of these experiments, a toxicity testing protocol was developed that involved growth of cultures in nutrient broth with tetracycline, storage of cultures at 4 degrees C, cell activation by reinoculation into nutrient broth, and toxicity testing by cell injection into the test media. Effective use of this approach required standardized time intervals for cell growth, storage, activation and exposure in the test media. Bioluminescence from Shk1 cells was measured in nutrient broth and influent wastewater and activated sludge mixed liquor from a municipal wastewater treatment plant. Using the Shk1 toxicity testing protocol, Zn EC(50) values for bioluminescence in nutrient broth, influent wastewater, and activated sludge mixed liquor were approximately 42, 7, and 32 mg/l, respectively. Zn concentrations as low as 1 mg/l could be detected in influent wastewater. The detection limit in influent wastewater is below the Zn concentrations typically reported to affect the activated sludge process.

Noninvasive quantitative measurement of bacterial growth in porous media under unsaturated-flow conditions

Glucose-dependent growth of the luxCDABE reporter bacterium Pseudomonas fluorescens HK44 was monitored noninvasively in quartz sand under unsaturated-flow conditions within a 45- by 56- by 1-cm two-dimensional light transmission chamber. The spatial and temporal development of growth were mapped daily over 7 days by quantifying salicylate-induced bioluminescence. A nonlinear model relating the rate of increase in light emission after salicylate exposure to microbial density successfully predicted growth over 4 orders of magnitude (r(2) = 0.95). Total model-predicted growth agreed with growth calculated from the mass balance of the system by using previously established growth parameters of HK44 (predicted, 1.2 x 10(12) cells; calculated, 1.7 x 10(12) cells). Colonization expanded in all directions from the inoculation region, including upward migration against the liquid flow. Both the daily rate of expansion of the colonized zone and the population density of the first day's growth in each newly colonized region remained relatively constant throughout the experiment. Nonetheless, substantial growth continued to occur on subsequent days in the older regions of the colonized zone. The proportion of daily potential growth that remained within the chamber declined progressively between days 2 and 7 (from 97 to 13%). A densely populated, anoxic region developed in the interior of the colonized zone even though the sand was unsaturated and fresh growth medium continued to flow through the colonized zone. These data illustrate the potential of a light transmission chamber, bioluminescent bacteria, and sensitive digital camera technology to noninvasively study real-time hydrology-microbiology interactions associated with unsaturated flow in porous media.

Exposing culprit organic pollutants: a review

There is a continuing need for monitoring the health of the environment due to the presence of pollutants. Here, we review the development and attributes of biosensors by which bacteria have been genetically modified to express the luminescence genes, i.e. to glow, in a quantified manner, in response to pollutants. We have concentrated on the detection of organic hydrocarbon pollutants and discussed the molecular mechanisms by which some of these chemicals act as effector molecules on the respective regulatory systems. The future of environmental biosensors is predictably bright. As more knowledge is gathered on the sensing regulatory component, the possibility of developing targeted or pollutant-specific biosensors is promising. Moreover, the repertoire of biosensors for culprit organic pollutants is expected to be enlarged through advances in genomics technology and identification of new sensory or receptor molecules. The need for pollutant detection at concentrations in the parts per trillion range or biosensors configured in a nanoscale is anticipated.

A transcriptional luxAB reporter fusion responding to fluorene in Sphingomonas sp. LB126 and its initial characterisation for whole-cell bioreporter purposes

The promoter probe mini-Tn5-luxAB-tet was used to create a luxAB transcriptional fusion responding to fluorene in the fluorene utilising bacterium Sphingomonas sp. LB126. The mutant strain, named L-132, was impaired in fluorene utilisation and strongly emitted light upon addition of fluorene to the growth medium. L-132 was initially characterised and examined for its potential use as a whole-cell biosensor in the perspective of quantifying fluorene in environmental samples. Activity of the reporter gene as a response to fluorene was detectable after 30 min and was optimal after 4 h. A linear response to fluorene concentrations within the water solubility range was achieved, with a detection limit of 200 microg per litre. Besides fluorene, L-132 weakly responded to the polycyclic aromatic hydrocarbons phenanthrene and dibenzothiophene, whereas strong responses were obtained with 9-fluorenone, 9-hydroxyfluorene, phthalic acid and protocatechuic acid. The latter four compounds are metabolites formed in course of fluorene degradation, which suggested that a fluorene metabolite rather than fluorene itself was the true inducer of the luxAB fusion in L-132.

A model that uses the induction phase of lux gene-dependent bioluminescence in Pseudomonas fluorescens HK44 to quantify cell density in translucent porous media

A cooled charge-coupled device (CCD) camera was used to follow the kinetics of induction of lux gene-dependent bioluminescence in Pseudomonas fluorescens HK44 held either in aqueous suspensions minus sand, saturated or unsaturated translucent sand (0.348 and 0.07 cm(3) H(2)O/cm(3) of sand, respectively), and at cell densities ranging between 1 x 10(6) and 8.5 x 10(8) cells/ml. Before O(2) availability became a limiting factor, the rate of light emission (L) increased with the square of time (t) and linearly with increasing cell density (c). A nonlinear model was developed that contains a "rate of increase in light emission" constant, B', which is determined directly from the slope of a plot of radical L/c against t. The model predicted the behavior of lux induction in HK44 under a variety of conditions. Similar B' values were determined [49.0-57.6 x 10(-10) light units/(cell min(2))] for cell suspensions held in aqueous medium minus sand, in saturated or unsaturated 40/50 grade sand (0.36 mm grain diameter) and in two other textural classes of translucent sand. Although both the growth phase, and the presence of glucose during lux induction affected the first detectable time (FDT) of bioluminescence by HK44 in sand, the kinetics of induction of light emission were similar among treatments (stationary phase cells plus glucose, B'=61.6+/-3.2, log phase cells plus glucose, B'=63.2+/-7.2). The potential exists to use a combination of a CCD camera system, an inducible lux gene containing bioluminescent bacterium, and a light transmission chamber to nonintrusively visualize and quantify in real time the interactions between bacterial growth and unsaturated flow of water and solutes in porous media.